Hi,
On Fri, Nov 25, 2011 at 1:28 AM, Puspita Halder <puspitah.gmail.com> wrote:
> the older version of Amber. Then I installed the Ambertool 1.2 to check
In general you're probably better off using the latest version of
AmberTools with all bugfixes applied,
http://ambermd.org/AmberTools-get.html and
http://ambermd.org/bugfixesat.html respectively.
> Checking coordinates: H107Y_eq1_new_300.dcd.bz2
> WARNING in checkCoordinates(): The actual number of atoms (46844)
> does not match the expected number of atoms (19) in
> (H107Y_eq1_new_300.dcd.bz2)
> With this version of the code, this will likely lead to program failure!!!
> It talks about atom numbers mismatch between the psf and the dcd file which
> is not understandable to me. Is there any atom number limitations for
> running ptraj? I used the same psf and dcd files for some of the analysis
There is no atom # limitation in ptraj; the issue here is that
according to ptraj the PSF file you have given it has information for
19 atoms, while there are 46844 atoms present in the given trajectory
file. So ptraj is allocating memory space for 19 atoms, then
attempting to read in coordinates for way more atoms, which leads to
the segmentation fault. If the PSF actually has info for all of your
atoms, then for some reason ptraj has an issue reading it; could you
send it to me so I can do some testing? Otherwise, make sure you are
giving ptraj a PSF file that corresponds to your trajectory.
-Dan
--
-------------------------
Daniel R. Roe, PhD
Postdoctoral Associate
BioMaPS Institute, Rutgers University
610 Taylor Road
Piscataway, NJ 08854
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Received on Mon Nov 28 2011 - 08:30:02 PST
